SOAPdenovo-Trans

[…] and viral factors. additional pipelines for analyzing the host splicing patterns may help us to understand the virus-host interaction and co-evolution in the future., raw reads were assembled using soapdenovo-trans with the following settings: “-k 31 –i 20 -e 3 –m 3 –l 100”. we then searched for matches against a customized virus database (described below) using the basic local alignment search […]

[…] read archive (sra no. srp077042). after removal of adaptor sequences and low-quality reads, we obtained 25.53 gb of clean data. subsequently, these clean data were assembled into 105,127 unigenes by soapdenovo-trans []. lengths of the unigenes ranged from 150 to 34,811 nt, with an average length of 682 nt and the n50 size of 1,257 nt ()., to predict the function classification and annotation […]

[…] of in silico reads using a perl script housed in the trinity software package, the reduced reads were assembled following the steps described in , using three different assemblers: trinity, soapdenovo-trans, and velvet. the consensus set of unigenes of the three different methods was used as the final representative transcriptome assembly, which resulted in 89,754 unigenes with a n50 […]

[…] with 72 bases length using casava 1.8 package tool provided by illumina. reads’ quality was assessed using filter tool. high quality reads were used for de novo assembly till scaffold level using soapdenovo-trans tool for three tea cultivars separately. k-mer size of 61 was selected for each of the assembly as it achieved the best balance between the numbers of transcripts produced, average […]

[…] (agilent technologies, usa), then libraries were sequenced on illumina gaiix platform. raw reads were trimmed and filtered with trimmomatic []. the assembly of transcriptome was performed using soapdenovo-trans transcriptome assembler. assembled transcripts were mapped to l. usitatissimum ‘reference’ transcriptome database of jgi genome portal with blastn (phytozomev11: […]

[…] performed using read quality filtering tool, filter in which poor quality reads and adapter contaminated reads were filtered-out. de novo assembly of good quality reads was performed using assembler soapdenovo-trans (http://soap.genomics.org.cn) which was run on different k-mer sizes ranging from 19–71 based on good quality read sequences and corresponding contigs/scaffolds were produced […]

[…] of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome., to improve the assembly quality, three computational tools (trinity, oases and soapdenovo-trans) were employed to enhance individual transcriptome assembly, and cap3 and cd-hit-est software were then used to merge these three assembled transcriptomes. in addition, functional […]

[…] shotgun assembly (tsa) database. additionally, transcripts of rhagophthalmus sp., chauliognathus flavipes and phrixothrix hirtus were downloaded from the sra archive and assembled using soapdenovo-trans-31mer 1.04 []. lantern and body transcripts of p. hirtus were merged into a single dataset (additional file : table s4) []. raw data were first examined in fastqc […]

[…] ambiguous bases (ns) or more than 50 low quality bases []. transcriptome assembly from the remaining reads followed the de bruijn graph algorithm as detailed in misof et al. [] by using the software soapdenovo-trans-31 kmer version 1.01 []. furthermore, the assembly was cleaned from remaining linker/adapter and foreign contaminations, such as vector, phage or bacterial sequences by checking […]

[…] information (ncbi) under accession srp071001 of bioproject prjna312361 and biosample samn04497582., assembly of all reads was done as described previously using the assemblers abyss and soapdenovo-trans with every kmer ending in 1 and 5 (-k program switch) from 21 to 95 [–]. resulting contigs were re-assembled by a pipeline of blastn and cap3 assembler [] as described earlier []. […]